Molecule of the Month: Non-Homologous End Joining Supercomplexes

DNA is the carrier of our genetic information. Because of its central importance, our DNA also possesses instructions for repairing itself when its strands become fractured. Breaks in DNA can be caused in many ways, for example, through errors in replication and by damage by external dangers such as radiation, oxidative stress and reactive chemicals. If only a single DNA strand is broken, repair systems in the nucleus smoothly fill the gap by using the complementary strand as a guide. Double-strand breaks, however, are more difficult to repair and are lethal to cells if left unfixed. Non-homologous end joining (NHEJ) is one of the major ways of reconnecting these broken ends to correct these harmful errors. This process is essential because in our everyday lives, about 10 double-strand breaks occur in each cell every day.

Non-homologous end joining is performed by a diverse collection of repair proteins that assemble step-by-step on the broken ends, forming supercomplexes that reconnect the DNA. Assembly of these supercomplexes begins with a heterodimer of two proteins, Ku70 and Ku80, that identifies the broken ends and recruits the other NHEJ proteins. The structure shown here captures the complex at the beginning of the process, when Ku70 and Ku80 have bound to the broken ends (PDB ID 1jey). DNA-PKcs will bind next (see PDB ID 6zhe, not shown), and then recruit many other enzymes to trim and prepare the two broken ends. The two ends are brought together by XRCC4 and XLF, and finally, DNA ligase IV glues the broken DNA strands together and releases the repaired DNA.

Double-strand breaks can have different problems, including spatial separation of the two ends, modified bases, and overhanging single strands at the broken ends. To deal with this, DNA-PKcs binds to the supercomplex (shown here from PDB ID 7nfc and 3w1b) and recruits other enzymes to repair different types of damage and bring the ends together. These include several small polymerases that fill in missing nucleotides and nucleases like Artemis that trim overhanging strands. Because of these multiple repairs at the damaged ends, NHEJ is not an exact process and may introduce small errors at the join site.

Finally, when the ends are properly prepared, the assembly is rearranged and DNA ligase IV reconnects them (PDB entry 7lsy). Even though double-strand breaks are harmful to a living organism, they also can be a benefit. For example, in our own immune system, antibody genes are broken and recombined with NHEJ to generate diversity, searching for new combinations that recognize new pathogens. Double-strand breaks are also a key part of cancer radiation therapy and chemotherapy. These therapies break the DNA in the targeted tumor cells, effectively killing them or slowing their growth. Unfortunately, the error-prone nature of NHEJ can also be a cause of cancer, by introducing carcinogenic errors in key genes involved in cellular growth and regulation.